diff --git a/cmd/flux/tree_kustomization.go b/cmd/flux/tree_kustomization.go
index c471295f..bf770cc6 100644
--- a/cmd/flux/tree_kustomization.go
+++ b/cmd/flux/tree_kustomization.go
@@ -272,5 +272,17 @@ func getHelmReleaseInventory(ctx context.Context, objectKey client.ObjectKey, ku
 		return nil, fmt.Errorf("failed to read the Helm storage object for HelmRelease '%s': %w", objectKey.String(), err)
 	}
 
+	for _, obj := range objects {
+		if obj.GetNamespace() == "" {
+			if isNamespaced, _ := utils.IsAPINamespaced(obj, kubeClient.Scheme(), kubeClient.RESTMapper()); isNamespaced {
+				if hr.Spec.TargetNamespace != "" {
+					obj.SetNamespace(hr.Spec.TargetNamespace)
+				} else {
+					obj.SetNamespace(hr.GetNamespace())
+				}
+			}
+		}
+	}
+
 	return object.UnstructuredSetToObjMetadataSet(objects), nil
 }
diff --git a/internal/utils/objectutil.go b/internal/utils/objectutil.go
new file mode 100644
index 00000000..35b381bc
--- /dev/null
+++ b/internal/utils/objectutil.go
@@ -0,0 +1,63 @@
+/*
+Copyright 2023 The Flux authors
+Copyright 2018 The Kubernetes Authors.
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+// TODO: Remove this when
+// https://github.com/kubernetes-sigs/controller-runtime/blob/c783d2527a7da76332a2d8d563a6ca0b80c12122/pkg/client/apiutil/apimachinery.go#L76-L104
+// is included in a semver release.
+
+package utils
+
+import (
+	"errors"
+	"fmt"
+
+	apimeta "k8s.io/apimachinery/pkg/api/meta"
+	"k8s.io/apimachinery/pkg/runtime"
+	"k8s.io/apimachinery/pkg/runtime/schema"
+	"sigs.k8s.io/controller-runtime/pkg/client/apiutil"
+)
+
+// IsAPINamespaced returns true if the object is namespace scoped.
+// For unstructured objects the gvk is found from the object itself.
+func IsAPINamespaced(obj runtime.Object, scheme *runtime.Scheme, restmapper apimeta.RESTMapper) (bool, error) {
+	gvk, err := apiutil.GVKForObject(obj, scheme)
+	if err != nil {
+		return false, err
+	}
+
+	return IsAPINamespacedWithGVK(gvk, scheme, restmapper)
+}
+
+// IsAPINamespacedWithGVK returns true if the object having the provided
+// GVK is namespace scoped.
+func IsAPINamespacedWithGVK(gk schema.GroupVersionKind, scheme *runtime.Scheme, restmapper apimeta.RESTMapper) (bool, error) {
+	restmapping, err := restmapper.RESTMapping(schema.GroupKind{Group: gk.Group, Kind: gk.Kind})
+	if err != nil {
+		return false, fmt.Errorf("failed to get restmapping: %w", err)
+	}
+
+	scope := restmapping.Scope.Name()
+
+	if scope == "" {
+		return false, errors.New("scope cannot be identified, empty scope returned")
+	}
+
+	if scope != apimeta.RESTScopeNameRoot {
+		return true, nil
+	}
+	return false, nil
+}
diff --git a/internal/utils/utils.go b/internal/utils/utils.go
index a1cb9a3d..ab9abe2e 100644
--- a/internal/utils/utils.go
+++ b/internal/utils/utils.go
@@ -54,9 +54,6 @@ import (
 	"github.com/fluxcd/flux2/pkg/manifestgen/install"
 )
 
-type Utils struct {
-}
-
 type ExecMode string
 
 const (